You are talking Wordpress? If so, you will not see the CSS files referenced in the header.php template because a function is being used to add the CSS file(s) to the output. Something like wp_enqueue_style() or another function. Look in your functions.php file for that function or similar.
What you are seeing is what the browser has taken from your host files to build the site, as the other poster has said your css is in a different place.